Variant report

Variant	rs1229564
Chromosome Location	chr7:97428673-97428674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1229534	0.81[ASN][1000 genomes]
rs1229535	0.81[ASN][1000 genomes]
rs1229538	0.81[ASN][1000 genomes]
rs1234947	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457585	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2530121	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2530122	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs2530123	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2665438	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971012	0.85[JPT][hapmap]
rs73140932	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888757	chr7:97003503-97461115	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1017392	chr7:97385921-97438035	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428178	chr7:97402756-97648029	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1017573	chr7:97420637-97452527	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1229564	C7orf52	cis	parietal	SCAN
rs1229564	GAL3ST4	cis	cerebellum	SCAN
rs1229564	PILRB	cis	cerebellum	SCAN
rs1229564	PILRB	cis	parietal	SCAN
rs1229564	GJC3	cis	parietal	SCAN
rs1229564	SPDYE3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97427000-97428800	Enhancers	Duodenum Mucosa	Duodenum
2	chr7:97428000-97428800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:97428200-97428800	Enhancers	Colonic Mucosa	Colon

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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